FMO DATABASE

FMODB ID: Z63QN

Calculation Name: 2NYX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NYX

Chain ID: A

ChEMBL ID:

UniProt ID: P71672

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1132654.160617
FMO2-HF: Nuclear repulsion	1077976.837498
FMO2-HF: Total energy	-54677.323119
FMO2-MP2: Total energy	-54839.329089

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:7:PRO)

Summations of interaction energy for fragment #1(A:7:PRO)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
13.892	-1.482	-0.172	16.559	-1.013	-0.006

Interaction energy analysis for fragmet #1(A:7:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : 0.007

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	9	THR	0	-0.068	-0.052	2.500	15.824	0.397	-0.171	16.571	-0.973	-0.006
4	A	10	ALA	0	0.004	0.012	5.254	-0.473	-0.420	-0.001	-0.012	-0.040	0.000
5	A	11	GLU	-1	-0.918	-0.987	8.106	-0.026	-0.026	0.000	0.000	0.000	0.000
6	A	12	GLU	-1	-0.967	-0.987	9.099	-0.945	-0.945	0.000	0.000	0.000	0.000
7	A	13	SER	0	0.022	0.014	12.320	0.083	0.083	0.000	0.000	0.000	0.000
8	A	14	VAL	0	0.081	0.013	16.096	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.891	-0.932	18.599	-0.205	-0.205	0.000	0.000	0.000	0.000
10	A	16	VAL	0	0.015	0.006	14.233	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	17	ILE	0	-0.003	0.006	13.530	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	18	THR	0	-0.022	-0.022	15.868	0.030	0.030	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.891	-0.942	18.738	-0.248	-0.248	0.000	0.000	0.000	0.000
14	A	20	ALA	0	-0.033	-0.021	15.223	0.011	0.011	0.000	0.000	0.000	0.000
15	A	21	LEU	0	-0.005	-0.008	17.064	0.022	0.022	0.000	0.000	0.000	0.000
16	A	22	LEU	0	0.011	0.023	18.966	0.027	0.027	0.000	0.000	0.000	0.000
17	A	23	THR	0	-0.015	0.013	19.735	0.024	0.024	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.016	0.008	18.272	0.017	0.017	0.000	0.000	0.000	0.000
19	A	25	SER	0	-0.066	-0.063	20.372	0.027	0.027	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.970	0.974	23.635	0.163	0.163	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.013	0.020	20.604	0.011	0.011	0.000	0.000	0.000	0.000
22	A	28	LEU	0	0.022	0.005	21.672	0.016	0.016	0.000	0.000	0.000	0.000
23	A	29	VAL	0	-0.007	0.000	25.269	0.014	0.014	0.000	0.000	0.000	0.000
24	A	30	ALA	0	0.006	0.012	27.221	0.009	0.009	0.000	0.000	0.000	0.000
25	A	31	ILE	0	0.009	0.015	24.138	0.009	0.009	0.000	0.000	0.000	0.000
26	A	32	SER	0	-0.062	-0.046	28.545	0.013	0.013	0.000	0.000	0.000	0.000
27	A	33	ALA	0	-0.017	-0.005	31.017	0.006	0.006	0.000	0.000	0.000	0.000
28	A	34	HIS	0	0.047	0.022	31.323	0.003	0.003	0.000	0.000	0.000	0.000
29	A	35	SER	0	-0.022	-0.023	31.539	0.007	0.007	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.055	-0.038	34.155	0.005	0.005	0.000	0.000	0.000	0.000
31	A	37	ALA	0	0.027	0.021	36.704	0.003	0.003	0.000	0.000	0.000	0.000
32	A	38	GLN	0	-0.045	-0.010	36.325	0.003	0.003	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.111	-0.044	38.155	0.004	0.004	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.916	-0.995	40.510	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.939	-0.959	41.302	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	42	ASN	0	-0.005	0.003	42.611	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	43	ILE	0	-0.093	-0.012	40.116	0.001	0.001	0.000	0.000	0.000	0.000
38	A	44	THR	0	0.037	0.004	41.053	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	45	ILE	0	0.066	0.017	35.905	0.002	0.002	0.000	0.000	0.000	0.000
40	A	46	PRO	0	-0.025	-0.021	38.553	0.003	0.003	0.000	0.000	0.000	0.000
41	A	47	GLN	0	0.069	0.022	40.659	0.003	0.003	0.000	0.000	0.000	0.000
42	A	48	PHE	0	0.072	0.038	34.285	0.004	0.004	0.000	0.000	0.000	0.000
43	A	49	ARG	1	0.902	0.946	35.593	0.013	0.013	0.000	0.000	0.000	0.000
44	A	50	THR	0	-0.008	0.001	37.949	0.005	0.005	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.019	0.000	40.351	0.003	0.003	0.000	0.000	0.000	0.000
46	A	52	VAL	0	0.011	0.011	34.183	0.003	0.003	0.000	0.000	0.000	0.000
47	A	53	ILE	0	-0.021	0.000	37.560	0.005	0.005	0.000	0.000	0.000	0.000
48	A	54	LEU	0	0.021	0.000	38.710	0.004	0.004	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.035	-0.015	37.686	0.002	0.002	0.000	0.000	0.000	0.000
50	A	56	ASN	0	-0.100	-0.049	33.786	0.005	0.005	0.000	0.000	0.000	0.000
51	A	57	HIS	0	-0.021	-0.006	36.658	0.005	0.005	0.000	0.000	0.000	0.000
52	A	58	GLY	0	-0.006	0.015	40.195	0.002	0.002	0.000	0.000	0.000	0.000
53	A	59	PRO	0	-0.046	-0.037	43.331	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	60	ILE	0	0.040	0.038	42.782	0.002	0.002	0.000	0.000	0.000	0.000
55	A	61	ASN	0	-0.007	0.007	46.795	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	62	LEU	0	0.046	-0.001	47.442	0.000	0.000	0.000	0.000	0.000	0.000
57	A	63	ALA	0	-0.011	0.006	47.575	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	64	THR	0	0.033	0.007	43.370	0.000	0.000	0.000	0.000	0.000	0.000
59	A	65	LEU	0	0.033	0.005	42.585	0.000	0.000	0.000	0.000	0.000	0.000
60	A	66	ALA	0	-0.019	-0.008	42.730	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	67	THR	0	-0.013	-0.002	41.137	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	68	LEU	0	-0.001	-0.001	37.350	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.058	-0.031	38.199	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	70	GLY	0	0.011	0.027	39.392	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	71	VAL	0	-0.070	-0.023	40.516	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	72	GLN	0	0.068	0.024	43.802	0.004	0.004	0.000	0.000	0.000	0.000
67	A	73	PRO	0	0.069	0.009	47.415	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	74	SER	0	-0.030	-0.011	49.461	0.000	0.000	0.000	0.000	0.000	0.000
69	A	75	ALA	0	0.025	0.004	47.853	0.000	0.000	0.000	0.000	0.000	0.000
70	A	76	THR	0	0.012	0.011	46.443	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	77	GLY	0	0.022	0.014	48.183	0.000	0.000	0.000	0.000	0.000	0.000
72	A	78	ARG	1	0.977	0.990	51.218	0.014	0.014	0.000	0.000	0.000	0.000
73	A	79	MET	0	-0.030	-0.006	43.574	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	80	VAL	0	0.024	0.004	47.757	0.000	0.000	0.000	0.000	0.000	0.000
75	A	81	ASP	-1	-0.887	-0.951	49.401	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.935	0.975	49.578	0.015	0.015	0.000	0.000	0.000	0.000
77	A	83	LEU	0	0.012	0.003	44.900	0.000	0.000	0.000	0.000	0.000	0.000
78	A	84	VAL	0	-0.026	0.001	49.125	0.001	0.001	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.004	0.011	52.172	0.000	0.000	0.000	0.000	0.000	0.000
80	A	86	ALA	0	-0.050	-0.018	49.224	0.000	0.000	0.000	0.000	0.000	0.000
81	A	87	GLU	-1	-0.923	-0.955	50.292	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	88	LEU	0	-0.058	-0.048	44.844	0.001	0.001	0.000	0.000	0.000	0.000
83	A	89	ILE	0	-0.065	-0.040	45.623	0.002	0.002	0.000	0.000	0.000	0.000
84	A	90	ASP	-1	-0.850	-0.902	48.951	0.003	0.003	0.000	0.000	0.000	0.000
85	A	91	ARG	1	0.846	0.892	50.983	0.001	0.001	0.000	0.000	0.000	0.000
86	A	92	LEU	0	0.009	0.001	50.978	0.000	0.000	0.000	0.000	0.000	0.000
87	A	93	PRO	0	0.013	0.004	54.713	0.000	0.000	0.000	0.000	0.000	0.000
88	A	94	HIS	0	0.031	0.017	52.339	0.001	0.001	0.000	0.000	0.000	0.000
89	A	95	PRO	0	0.011	0.018	53.472	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	96	THR	0	0.028	-0.004	56.426	0.001	0.001	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.035	-0.004	56.759	0.000	0.000	0.000	0.000	0.000	0.000
92	A	98	ARG	1	0.898	0.937	58.764	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	99	ARG	1	0.937	0.995	58.239	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	100	GLU	-1	-0.838	-0.913	53.098	0.014	0.014	0.000	0.000	0.000	0.000
95	A	101	LEU	0	-0.037	-0.035	53.012	0.000	0.000	0.000	0.000	0.000	0.000
96	A	102	LEU	0	0.023	-0.010	49.794	0.000	0.000	0.000	0.000	0.000	0.000
97	A	103	ALA	0	0.000	0.015	47.648	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	104	ALA	0	0.041	0.009	46.624	0.002	0.002	0.000	0.000	0.000	0.000
99	A	105	LEU	0	-0.032	0.003	41.587	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	106	THR	0	0.065	0.056	46.295	0.002	0.002	0.000	0.000	0.000	0.000
101	A	107	LYS	1	0.867	0.909	46.546	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	108	ARG	1	1.038	1.010	44.200	0.009	0.009	0.000	0.000	0.000	0.000
103	A	109	GLY	0	0.092	0.049	44.498	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	110	ARG	1	0.912	0.949	42.037	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	111	ASP	-1	-0.856	-0.921	40.945	0.002	0.002	0.000	0.000	0.000	0.000
106	A	112	VAL	0	-0.016	0.000	40.255	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	113	VAL	0	0.020	0.007	36.575	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	114	ARG	1	0.939	0.962	36.001	-0.021	-0.021	0.000	0.000	0.000	0.000
109	A	115	GLN	0	0.061	0.030	36.062	0.002	0.002	0.000	0.000	0.000	0.000
110	A	116	VAL	0	0.016	0.029	33.863	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	117	THR	0	-0.064	-0.041	31.041	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	118	GLU	-1	-0.904	-0.964	31.259	0.000	0.000	0.000	0.000	0.000	0.000
113	A	119	HIS	0	0.019	0.024	32.044	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	120	ARG	1	0.940	0.973	26.487	0.021	0.021	0.000	0.000	0.000	0.000
115	A	121	ARG	1	0.926	0.954	27.054	-0.021	-0.021	0.000	0.000	0.000	0.000
116	A	122	THR	0	0.007	0.012	27.021	0.000	0.000	0.000	0.000	0.000	0.000
117	A	123	GLU	-1	-0.825	-0.899	26.698	-0.089	-0.089	0.000	0.000	0.000	0.000
118	A	124	ILE	0	-0.020	-0.025	22.119	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	125	ALA	0	-0.015	0.000	22.768	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	126	ARG	1	0.904	0.947	23.333	0.094	0.094	0.000	0.000	0.000	0.000
121	A	127	ILE	0	-0.038	-0.021	19.958	-0.013	-0.013	0.000	0.000	0.000	0.000
122	A	128	VAL	0	0.012	-0.013	18.435	-0.019	-0.019	0.000	0.000	0.000	0.000
123	A	129	GLU	-1	-0.987	-0.986	18.569	-0.048	-0.048	0.000	0.000	0.000	0.000
124	A	130	GLN	0	-0.058	-0.024	19.297	0.014	0.014	0.000	0.000	0.000	0.000
125	A	131	MET	0	-0.043	0.004	14.105	-0.018	-0.018	0.000	0.000	0.000	0.000
126	A	132	ALA	0	0.048	0.023	11.303	0.065	0.065	0.000	0.000	0.000	0.000
127	A	133	PRO	0	-0.005	-0.028	12.919	0.009	0.009	0.000	0.000	0.000	0.000
128	A	134	ALA	0	0.027	0.006	8.171	0.055	0.055	0.000	0.000	0.000	0.000
129	A	135	GLU	-1	-0.869	-0.930	9.597	-0.450	-0.450	0.000	0.000	0.000	0.000
130	A	136	ARG	1	0.866	0.938	10.906	0.067	0.067	0.000	0.000	0.000	0.000
131	A	137	HIS	0	0.005	-0.003	11.314	0.042	0.042	0.000	0.000	0.000	0.000
132	A	138	GLY	0	0.014	0.008	9.650	0.057	0.057	0.000	0.000	0.000	0.000
133	A	139	LEU	0	0.008	0.012	10.438	-0.024	-0.024	0.000	0.000	0.000	0.000
134	A	140	VAL	0	0.015	0.005	13.676	0.004	0.004	0.000	0.000	0.000	0.000
135	A	141	ARG	1	0.969	1.000	8.928	-0.382	-0.382	0.000	0.000	0.000	0.000
136	A	142	ALA	0	-0.004	-0.002	12.277	0.004	0.004	0.000	0.000	0.000	0.000
137	A	143	LEU	0	0.007	-0.007	13.868	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	144	THR	0	-0.034	-0.015	16.917	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	145	ALA	0	0.003	0.006	15.093	0.007	0.007	0.000	0.000	0.000	0.000
140	A	146	PHE	0	-0.042	-0.022	17.147	-0.010	-0.010	0.000	0.000	0.000	0.000
141	A	147	THR	0	-0.080	-0.064	19.215	-0.009	-0.009	0.000	0.000	0.000	0.000
142	A	148	GLU	-1	-0.964	-0.971	20.041	0.141	0.141	0.000	0.000	0.000	0.000
143	A	149	ALA	0	-0.025	0.001	20.000	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	150	GLY	0	0.010	0.018	21.954	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	151	GLY	0	-0.048	-0.043	24.400	0.002	0.002	0.000	0.000	0.000	0.000
146	A	152	GLU	-1	-0.997	-0.981	25.301	0.075	0.075	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:7:PRO)